Eyes were fixed with 4% paraformaldehyde for 30 minutes before being transferred to 30% sucrose in PBS (control, n = 6; saline, n = 6; PDGF × 1, n = 4; PDGF × 2, n = 4). Eyes then were immersed in embedding capsules with the plica semilunaris perpendicular to the plane of sectioning. Retina sections of 14 μm thickness were collected through the dorsal-ventral/superior-inferior axis of the retina.
Slides were blocked in 10% normal goat serum (NGS) in PBS with 0.5% Triton X-100 for one hour at room temperature. Primary antibodies made up in buffer solution of 4% NGS in PBS with 0.3% Triton X-100 included antibodies against rabbit βIII-tubulin (1:1000; Covance Research Products, Inc., Denver, NJ, USA), mouse βIII-tubulin (1:2000; Promega, Madison, WI, USA), mouse NeuN (1:250; EMD Millipore, Billerica, MA, USA), mouse post-synaptic density protein 95 (PSD-95, 1:1000; Abcam, Cambridge, UK), chicken synaptophysin (SY38, 1:1000; Abcam), rabbit glutamate receptor-1 (GluR1, 1:50; Calbiochem, San Diego, CA, USA), guinea pig ionized calcium binding adaptor protein 1 (Iba-1; 1:500; Synaptic Systems, Göttingen, Germany), rabbit phospho-PDGF receptor α (pPDGFR, 1:50; Abcam), rabbit CD45 (1:300; Abcam). AlexaFluor-conjugated secondary antibodies (1:1000; Invitrogen, Carlsbad, CA, USA) then were added for one hour together with 4′,6-diamidino-2-phenylindole (DAPI) stain. Two slides also were stained in the absence of each primary antibody for use as negative controls.
Images were taken on a Leica SP5 confocal microscope at ×40 and ×63 magnification with z-step intervals of 0.3 μm. Open-source image processing software Fiji
21 was used to reconstruct z-stack projections of individual optical sections for quantification. Images for the quantification of synaptic marker density in the inner plexiform layer (IPL) were taken from six images per eye using ×40 magnification at the area bounded by the RGC layer (RGCL) and inner nuclear layer (INL), with the stack end-points set to visualize 4′,6-diamidino-2-phenylendole (DAPI)–stained nuclei at the RGCL. Only sections with the ONH clearly visible were chosen for analysis to ensure that the regions being assessed were equidistant from the ONH and along the superior–inferior axis, as far as possible. This is important, as topographical studies of rodent retinas have shown that the density of RGCs varies with distance from the ONH.
22 Confocal images were thresholded to the average of five positively-staining synaptic puncta for each channel, and counted using the automated Analyze Particle plug-in on Fiji which measured the total number of particles above the set threshold value. Only particles within the area bounded by the RGCL and INL (the IPL area) were counted. The z-stack volume was calculated by multiplying the z-step size by the number of slices per stack and the IPL area for each stack. The total particle count for all slices through the stack then was divided by the z-stack volume to obtain the synaptic density for each marker.
Retinal ganglion cell numbers were quantified based on the numbers of βIII-tubulin and DAPI-positive cells within the RGC layer. Retinal regions used in this analysis were equidistant from the optic nerve head and taken from at least four individual sections per eye. Tubulin fluorescent intensity within the IPL also was assessed within this region by measuring the fluorescent integrated density within at least eight 30 × 30 μm regions positioned between the RGCL and INL.
Differential levels of CD45 expression can be used to determine if Iba-1–positive cells are infiltrating monocytes from the peripheral circulation, which show high levels of CD45, or part of a resident microglial population that express CD45 at low levels.
23 Therefore, Iba-1–positive cells in retinal sections also were assessed for levels of CD45-expression and categorized as CD45
hi or CD45
lo based on the intensity of staining.
Analysis of longitudinal ONH sections focused on the laminar zone, which has been defined as a conical area bordered by the posterior sclera proximally and the start of the myelinated optic nerve distally.
24,25